Bonded excimer in stacked adenines:Semiclassical simulations

The nonradiative decay of a π-stacked pair of adenine molecules,one of which was excited by an ultrafast laser pulse,is studied by semiclassical dynamics simulations.This simulation investigation is focused on the effect of the formation of bonded excimer in stacked adenines on the mechanism of ultrafast decay.The simulation finds that the formation of the bonded excimer significantly lowers the energy gap between the LUMO and HOMO and consequently facilitates the deactivation of the electronically excited molecule.On the other hand,the formation of the chemical bond between two stacked adenines restricts the deformation vibration of the pyrimidine of the excited molecule due to the steric effect.This slows down the formation of the coupling between the HOMO and LUMO energy levels and therefore delays the deactivation process of the excited adenine molecule to the electronic ground state.     

The photoisomerization mechanism of azobenzene: a semiclassical simulation of nonadiabatic dynamics

We have simulated the photoisomerization dynamics of azobenzene, taking into account internal conversion and geometrical relaxation processes, by means of a semiclassical surface hopping approach. Both n-->pi* and pi-->pi* excitations and both cis-->trans and trans-->cis conversions have been considered. We show that in all cases the torsion around the N==N double bond is the preferred mechanism. The quantum yields measured are correctly reproduced and the observed differences are explained as a result of the competition between the inertia of the torsional motion and the premature deactivation of the excited state. Recent time-resolved spectroscopic experiments are interpreted in the light of the simulated dynamics.     

A simple correction to final state energies of doublet radicals described by equation-of-motion coupled cluster theory in the singles and doubles approximation

A computationally inexpensive energy correction is suggested for radicals described by the equation-of-motion coupled cluster method for ionized states in the singles and doubles approximation (EOMIP-CCSD). The approach is primarily intended for doublet states that are qualitatively described by Koopmans' approximation. Following a strategy similar to those used in multireference coupled cluster theory, the proposed correction accounts for all correlation effects through third order in perturbation theory and also includes selected contributions to higher-order energies. As an initial test of the numerical performance of the method, total energies and energy splittings are calculated for some small prototype radicals.     

Two-Term and multi-term approximation of the nonstationary electron velocity distribution in an electric field in a gas

A very efficient, strict nonstationary multi-term approach has been developed as a generalization of the conventional and the strict nonstationary two-term approximations used for solving the nonstationary , electron Boltzmann equation. As a first application the temporal relaxation of electrons in a model plasma acted upon by a de electric field has been investigated. The results are compared with corresponding ones obtained by the conventional and the strict nonstationary two-term approach as well as with very accurate Monte Carlo simulations. Perfect agreement between nonstationary eight-term Boltzmann and Monte Carlo calculations is found.     

New developments in theory of fast electron scattering in solids: Applications to microbeam analysis

The study of fast electron interaction with solids in the energy range from 100 eV to several tens of keV is prompted by quickly developing microbeam analysis techniques such as electron probe microanalysis, scanning electron microscopy, electron energy loss spectroscopy and so on. It turned out that for random solids the electron transport problem might be solved on the basis of the generalized radiative field similarity principle. The latter states that the exact differential elastic cross section in the kinetic equation may be replaced by an approximate one provided the conditions of radiative field similarity are fulfilled. Application of the generalized similarity principle to electron scattering in solids has revealed many interesting features of electron transport. Easy to use and effective formulae have been obtained for the angular and energy distribution of electrons leaving a target, total yields of characteristic photons and slow electrons escaping from a sample bombarded by fast primaries, escape probability of Auger electrons as a function of depth etc. The analytical results have been compared with Monte Carlo calculations and experiments in a broad range of electron energies and scattering properties of solids and good agreement has been observed.     

锐钛矿和金红石二氧化钛中光生载流子的超快动力学：电声相互作用研究

本文结合玻尔兹曼输运方程和电声散射速率计算研究锐钛矿和金红石二氧化钛中光生载流子的超快动力学过程. 其中,动力学模拟所需的结构参数均通过第一性原理计算获得. 结果表明,由于存在强Fröhlich型电声耦合,纵光学声子模对两个晶相的能量弛豫过程均有十分显著的影响,但是两个晶相的弛豫机理却表现出明显的差异. 对于单条导带内的弛豫过程,锐钛矿和金红石的能量弛豫时间分别为24.0 fs和11.8 fs,前者约为后者的二倍. 这一差异来源于两个晶相中不同的电子扩散分布以及不同的声学模散射贡献. 对于涉及多条导带的弛豫过程,预测的锐钛矿和金红石的总体弛豫时间分别为47 fs和57 fs,其相对大小与单条导带的情况相反. 分析表明金红石相弛豫较慢是因为存在多个速率控制步骤. 这些发现为调控电子动力学以及设计高效的二氧化钛器件提供了有价值的信息.     

Negative Electron Mobility in Attachment-Dominated Plasmas

The temporal evolution of the electron velocity-distribution function(EVDF), the concentration, mean energy, and the drift velocity of theelectrons is studied on a kinetic basis in a weakly ionized Ar/F₂mixture plasma under conditions when the electron concentration temporallydecreases as a result of the electron attachment to fluoride molecules. Usingan appropriate relaxation model, the time-dependent electron Boltzmannequation was solved in multiterm and two-term approximations of the velocitydistribution function. The multiterm results confirmed predictions on theoccurrence of negative electron mobilities in such a decaying Ar/F₂plasma, which were made in a former study using the conventional two-termapproximation. The investigations particularly showed that this approximationgives almost accurate results for the EVDF and related electron swarm parametersexcept for in the very beginning of the relaxation process. It has been furthershown that for a certain range of the reduced electric field strength, thedrift velocity becomes negative in the process of temporal evolution and remainsnegative even when approaching the hydrodynamic stage of the electronswarm. In addition, the role played by the back heating from the gas byelastic collisions on the EVDF formation is studied and various comparisonswith corresponding Monte Carlo results are performed.     

胰蛋白酶和苯酰氨类抑制剂结合自由能的预测

用基于线性响应近似的自由能预测方法计算胰蛋白酶和苯酰氨类抑制剂的结合 自由能。计算结果表明,单参数,双参数和三参数模型具有相似的线性回归系数, 但三参数和双参数模型的交互验证回归系数要明显优于单参数模型。从预测能力来 看,双参数模型和三参数模型都能够很好地预测测试集中抑制剂的结合自由能,其 中双参数模型预测的结果要略优于三参数模型的预测结果。对测试集中的抑制剂, 双参数模型预测得到的预测自由能和实际自由能之间平均绝对误差仅为1.15 kJ/mol。自由能计算模型以及分子动力学轨迹能很好地解释抑制剂结构和活性的 关系,为药物设计提供了重要的结构信息。     

A method for conformational sampling of loops in proteins based on adiabatic decoupling and temperature or force scaling

A method for conformational Boltzmann sampling of loops in proteins in aqueous solution is presented that is based on adiabatic decoupling molecular dynamics (MD) simulation with temperature or force scaling. To illustrate the enhanced sampling, the loop from residues 33 to 43 in the bovine protein ribonuclease A is adiabatically decoupled from the rest of the protein and the solvent with a mass scaling factor s(m) =1000 and the sampling is enhanced with a scaling of the temperature using s(T) =2 or of the force using s(V) =0.667. Over 5 ns of simulation the secondary structure of the protein remains unaltered while a combined dihedral-angle conformational cluster analysis shows an increase of conformations outside the first most populated cluster of loop conformations for adiabatic decoupling MD with temperature scaling using s(T) =2 or force scaling using s(V) =0.667 compared to the standard MD simulation. The atom-positional root-mean-square fluctuations of the C(α) atoms of the loop show an increase in the movement of the loop as well, indicating that adiabatic decoupling MD with upscaling of the temperature or downscaling of the force is a promising method for conformational Boltzmann sampling.